MolNFT v1 · #70504 · protein
Crystal structure of the ERBB3 kinase domain in complex with AMP-pnp
3LMG · Receptor tyrosine-protein kinase erbb-3: “Crystal structure of the ERBB3 kinase domain in complex with AMP-pnp”. X-ray diffraction, 2 ligands (ANP, MG), 5 pockets (best druggability 0.76). MolNFT v1 #70504 on GenesisL1: 3D…
- PDB
- 3LMG
- Type
- protein
- Length
- 536 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor tyrosine-protein kinase erbb-3
- EC
- 2.7.10.1
- UniProt
- P21860
- Ligands
- ANP, MG
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor tyrosine-protein kinase erbb-3 (EC 2.7.10.1) | protein | 268 | 40% helix, 19% strand | P21860 |
| B | Receptor tyrosine-protein kinase erbb-3 (EC 2.7.10.1) | protein | 268 | 39% helix, 18% strand | P21860 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.76 | 0.87 | 53 | empty |
| 2 | 317 | 0.70 | 0.83 | 35 | MG, ANP |
| 3 | 344 | 0.69 | 0.82 | 34 | MG, ANP |
| 4 | 131 | 0.54 | 0.81 | 18 | empty |
| 5 | 210 | 0.54 | 0.78 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 650 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3LMG · Crystal structure of the ERBB3 kinase domain in complex with AMP-PNP · the same entry in another collection · chain A against A, TM-score 1.00
- P21860 · AlphaFold monomer V2.0 prediction for receptor tyrosine-protein kinase erbb-3 (P21860) · a predicted model of the same protein · chain B against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P21860
- Elsewhere: RCSB PDB 3LMG · PDBe 3LMG · UniProt P21860
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